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The Top 23 Nanopore Open Source Projects

Open source projects categorized as Nanopore
Categories > Nanopore
Sniffles ⭐ 479
Structural variation caller using third generation sequencing
total releases 8most recent commit 4 months ago
Wtdbg2 ⭐ 401
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
most recent commit 3 years ago
Medaka ⭐ 359
Sequence correction provided by ONT Research
total releases 85most recent commit 5 months ago
Bonito ⭐ 354
A PyTorch Basecaller for Oxford Nanopore Reads
total releases 48most recent commit 5 months ago
Dorado ⭐ 309
Oxford Nanopore's Basecaller
most recent commit 3 months ago
Shasta ⭐ 269
[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
most recent commit 2 years ago
Pepper ⭐ 216
PEPPER-Margin-DeepVariant
total releases 8most recent commit 6 months ago
Pycoqc ⭐ 213
pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
total releases 50most recent commit 6 months ago
Clair3 ⭐ 191
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
most recent commit 3 months ago
Awesome Nanopore ⭐ 175
A curated list of awesome nanopore analysis tools.
most recent commit 5 months ago
Mag ⭐ 164
Assembly and binning of metagenomes
most recent commit 3 months ago
Gtz ⭐ 156
A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.
most recent commit 2 years ago
Genomics ⭐ 154
A collection of scripts and notes related to genomics and bioinformatics
most recent commit 2 years ago
Bambu ⭐ 150
Reference-guided transcript discovery and quantification for long read RNA-Seq data
most recent commit 5 months ago
Winnowmap ⭐ 131
Long read / genome alignment software
most recent commit 2 years ago
Nanoseq ⭐ 122
Nanopore demultiplexing, QC and alignment pipeline
most recent commit 7 months ago
Xpore ⭐ 122
Identification of differential RNA modifications from nanopore direct RNA sequencing
total releases 20most recent commit 5 months ago
Remora ⭐ 120
Methylation/modified base calling separated from basecalling.
dependent packages 1total releases 13most recent commit 5 months agopypi ont-remora} Downloads
Squigglekit ⭐ 106
SquiggleKit: A toolkit for manipulating nanopore signal data
most recent commit a year ago
Viralrecon ⭐ 101
Assembly and intrahost/low-frequency variant calling for viral samples
most recent commit 7 months ago
Isoquant ⭐ 98
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
most recent commit 4 months ago
Pod5 File Format ⭐ 97
Pod5: a high performance file format for nanopore reads.
dependent packages 1total releases 10most recent commit 4 months agopypi pod5-format} Downloads
Pipeline Transcriptome De ⭐ 95
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
most recent commit a year ago
The 5 Most Depended On Nanopore Open Source Projects
Pyspoa ⭐ 12
Python bindings to spoa
dependent packages 4total releases 14latest release October 04, 2023most recent commit 7 months agopypi pyspoa} Downloads
Pyguppyclient ⭐ 25
Python client library for Guppy
dependent packages 2total releases 11latest release May 24, 2021most recent commit 2 years agopypi pyguppyclient} Downloads
Pod5 File Format ⭐ 97
Pod5: a high performance file format for nanopore reads.
dependent packages 1total releases 10latest release November 07, 2022most recent commit 4 months agopypi pod5-format} Downloads
Remora ⭐ 120
Methylation/modified base calling separated from basecalling.
dependent packages 1total releases 13latest release December 05, 2023most recent commit 5 months agopypi ont-remora} Downloads
Slow5 Rs ⭐ 5
Low level bindings and wrapper for slow5lib, an alternative for ONT Nanopore sequencing FAST5 output
dependent packages 1total releases 11latest release September 04, 2023most recent commit 8 months agocargo slow5lib-sys} Downloads
The 10 Latest Releases In Nanopore Open Source Projects
Medaka ⭐ 359
Sequence correction provided by ONT Research
total releases 85latest release December 06, 2023most recent commit 5 months ago
Remora ⭐ 120
Methylation/modified base calling separated from basecalling.
dependent packages 1total releases 13latest release December 05, 2023most recent commit 5 months agopypi ont-remora} Downloads
Ontime ⭐ 11
Extract subsets of ONT (Nanopore) reads based on time
total releases 5latest release October 30, 2023most recent commit 6 months ago
Tbpore ⭐ 9
Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
total releases 11latest release October 11, 2023most recent commit 7 months ago
Pyspoa ⭐ 12
Python bindings to spoa
dependent packages 4total releases 14latest release October 04, 2023most recent commit 7 months agopypi pyspoa} Downloads
Sandy ⭐ 14
A straightforward and complete next-generation sequencing read simulator
total releases 9latest release September 19, 2023most recent commit 5 months ago
Slow5 Rs ⭐ 5
Low level bindings and wrapper for slow5lib, an alternative for ONT Nanopore sequencing FAST5 output
dependent packages 1total releases 11latest release September 04, 2023most recent commit 8 months agocargo slow5lib-sys} Downloads
Ampligone ⭐ 6
A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment
total releases 8latest release August 08, 2023most recent commit 9 months ago
Bonito ⭐ 354
A PyTorch Basecaller for Oxford Nanopore Reads
total releases 48latest release July 31, 2023most recent commit 5 months ago
Sniffles ⭐ 479
Structural variation caller using third generation sequencing
total releases 8latest release July 27, 2023most recent commit 4 months ago
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